Through the Gate
by Heartwing
Summary: Sequel to Strangers and Secrets. John Watson is visiting with his Aunt Janet, when an unexpected emergency occurs at the top secret Cheyenne Mountain. 2nd in the At Holmes and Away series. Series owes its title to thepinkpenguinparty
1. Chapter 1

**A/N: This is a sequel to my other Sherlock/SG-1 Crossover, _Strangers and Secrets_.**

**There are spoilers for the episodes Heroes Part 1 and Part 2.**

**Please note that I am not a doctor, nor do I play one on tv. All medical events are made up or copied from what I've seen on tv shows.**

**Also, I realize that the Stargate Program is a top secret military program and there is no way in hell anything like this would ever happen, but humor me, okay?**

**Please note that this is unbetaed and hasn't been britpicked. If anyone wants to volunteer, feel free :)**

* * *

After that incident in Egypt with the weird American military, John decided to take up his Aunt Janet's offer to visit. Harry and Clara were still in the newlywed stage and he always felt like a third wheel. He and Harry had never been very close to begin with, and while he liked Clara, he just wasn't comfortable with them. He had no other family in London, and had lost contact with all his Uni friends when he joined the Army, so he had no place else to stay.

He soon discovered that leave was much more bearable when he spent it with his Aunt Janet. While she would try to take off to spend time with him, she wasn't always able to. The days she couldn't, he'd wander around town and spend some time with her adopted daughter, Cassie. Sometimes in the evenings, they'd go to the pub with some of the airmen from her base. They shared war stories, jokes, and complained about their officers. John noticed that their stories were often vague, but he never pried, being in a few covert operations himself. He felt a little guilty not going home, but he could only handle so much with his overbearing sister.

During the pub nights, John became fairly close with the group he met in Egypt. Their relationship was a little awkward at time, because they all worked together and John wasn't allowed to know what exactly they did. He asked Carter once, but she just fed him an obviously false cover story and John never asked again. Despite the large secret between John and SG-1, they got along rather well and John came to look forward to his leaves.

John had stayed with Frasier for quite a few of his leaves, and was actually happy about this leave. Janet had managed to get a whole three days in a row off.

"You've got great timing, John. There's a film crew on base today," Frasier nodded at Cheyenne Mountain. John had met her outside the base, and they decided to walk on some of the trails nearby. They were normally only used by the SG teams, but the public was allowed to walk them. "They're making a documentary. I'm sure I'll have to sit through an interview at some point, but the less cameras I have following me around, the better."

"A documentary?" John asked, surprised. "A documentary on a top secret military base you're always very careful to not reveal anything about?"

Frasier grimaced. "It doesn't make a lot of sense to me, but I guess they want one in case they ever decide to go public with the program."

"Yes, deep space radar telemetry just fascinates the public," John grinned, remembering the cover story a scientist from the pub tried to feed him.

"I wouldn't be surprised," she smiled back. "You never know with fads. A future trend might be science and learning. Math clubs might be more popular than baseball."

"In your dreams, Aunt Janet," John laughed. They walked in silence for a while, enjoying the nice autumn afternoon, although John was a little on edge. After spending the majority of last few years in a desert, the forest made him a little claustrophobic. He didn't like not being able to see around him.

They both jumped when Janet's phone went off. "Doctor Frasier," she answered. Her smile dropped and her face paled as she listened. "Understood. I'll be there soon. Ten minutes, top," she started walking fast towards the mountain, John on her heels. "Inform the General that I'll be accompanied by my nephew, a British army surgeon." She listened to the other end, before snapping into soldier mode. "I don't care about clearance," she barked. "I'm going to need help and none of the other doctors in today have adequate field training. He'll be coming with. He's been in covert operations, he can keep a secret. Good," she snapped the phone shut and started jogging towards the base, John on her heels.

He was surprised. "How'd you know about the operations? Their security clearance is plenty high enough in my own government."

"John, the only person in this country with higher clearance than me is the General and the President. And the General doesn't dare keep things from me. I was curious about what you were up to."

John nodded. There'd be more time to ask about this later, but now he had to focus on the situation, whatever it was. "So what happened? Why do you need me?"

"We have a team in the field under enemy fire. They've been cut off from safety and some have been hit. They're trapped." Frasier sighed in relief as they reached the road. Only a few yards stood between them and the first checkpoint.

"I don't understand," John frowned, moving up next to her. "Under fire where?"

She glanced at him. "John, what I'm about to tell you is top secret. I could be court martialed for this. If you ever tell anyone, the military will arrest you, probably without trial, and hold you indefinitely. What I'm going to tell you isn't even going to sound real, but I promise it is. In short, there's a device we found in Egypt. It's called the Stargate, it was built by aliens and it allows us to travel to other planets." Frasier nodded at the guards when they reached the checkpoint, who waved her on with only a glance for John.

"Doctor, there's a jeep waiting for you," one of the airmen pointed. She nodded at him in thanks.

"Aliens," John stated, trying to figure out if she was serious or just winding him up. They climbed in the back of the jeep, where there was an older man sitting. A quick glance at his uniform showed John that he was very high up in the military food chain.

"Doctor Frasier, Doctor Watson," the man greeted.

"John, this is General Hammond," Frasier told him.

"Sir," John greeted courteously, fully aware this man was probably one of the most powerful in America.

The General nodded at John. "Son, whatever she told you is the God-honest truth. I don't think I need to explain to you just how secret this program is."

John decided to just take everything in stride and have is crisis later when there was more time. "No, sir," he respectfully nodded.

"Good man," Hammond clapped him on the shoulder. "You can sign a non-disclosure agreement later. For now, we've got a bigger problem."

"What exactly happened?" Frasier wanted to know. As they talked, the jeep had arrived at the base. They quickly climbed out and trotted inside, where they got in an elevator and headed down.

"SG-13 went through the gate yesterday to P3X-666. They got pinned down before they could get back. Senior Airman Wells was badly hurt and he can't be moved yet. I hope you're as good in the field as the reports say, son," the General added, turning to John. They stepped out of the elevator and hurried down the hallway to the armoury.

He nodded, not bothering to ask how he got ahold of British reports. "British Special Forces, sir," he added, realizing it was probably unnecessary.

"Good. SG-5 and 7 are going through the gate now. SG-1 will accompany you two."

An airman helped John and Frasier into their gear which, John was relieved to see, was very similar to his own. He wasn't too keen on the idea of some alien thing protecting him. He quickly looked through his pack to see where the different supplies were. It was, once again, very similar to his pack. That was good. He was handed a familiar assault rifle and a handgun. They weren't the same model as his, but they were close enough that he would be able to use them if he needed to.

As soon as they were suited up, they were hurried again towards the elevator, where they were met with SG-1. John was pleased to see it was the same group from Egypt. He had gotten to know them some from the pub visits, and was comfortable enough with them to trust they had his back. They were geared up already, and armed to the teeth. As they neared, John could see why Murray was wearing each time they met. His gold tattoo thing on his forehead was very conspicuous. John wondered why he didn't get it removed, and if it had something to do with the whole alien planet part of their job. Along with the usual guns, he was also holding a strange looking staff.

"What's he doing here, doc?" O'Neill asked Fraiser, looking startled to see John.

"He's coming with," she told them in a firm voice, not accepting any arguments.

O'Niell glanced at the General, who nodded. He turned back to John and eyed him up, assessing him. "Can I trust you to watch our backs, Watson?" he asked in a cold, unfriendly voice.

"Yes sir. I was in Special Forces. Do you have my back, sir?" John met his gaze evenly, not worried about the tone, knowing this was the only test O'Neill had time for. He had done the exact same with other soldiers he met only minutes before going into the fray. Being cold and unfriendly to see their reaction was the quickest was to get a read on another soldier.

"We do, Watson," O'Neill softened and nodded grimly, though in approval. "Carter, you ought to tell Watson what to expect when he goes through."

John turned to Carter, who quickly explained what the wormhole felt like, and what to expect when he arrived at the other side. Although he still didn't quite believe this, he decided to shove down his doubts and trust what she told him.

"Wow," John blinked in amazement as they entered the Gateroom. The stargate was huge and strangely beautiful. The wormhole was already established, and the circle was filled with a blue swirling gooey substance. He followed the team up the ramp where they got into position and readied their weapons. He watched them go through the gate and when it was his turn, he took a breath and stepped through.


	2. Chapter 2

**A/N: Part 2, the last chapter!**

**Probably should have mentioned before that this contains spoilers for the episode Heroes Part 1 and Part 2, though most of you probably have already noticed.**

**I plan on writing more stories in this universe, but it may be a while since I haven't even started them yet. I will post a third chapter here letting you guys know when it's up so you can just follow this and don't have to author alert me if you don't want.**

**Enjoy, and please review!**

* * *

As soon as he felt his feet touch grass, he dropped into a crouch before he even got his breath back. He took a very brief moment to breathe and take in his surroundings. He noticed Murray-or whatever his real name was- keeping an eye on him. He chose to ignore that, and followed Jackson and Janet across the field to some rocks and bushes. He could hear bullets being fired around him and zapping noises, but he tuned them out and kept going.

He didn't really like the zaps, but the sounds of guns reassured them and he fell into a familiar mindset. He was a soldier now, going towards someone who needed his help. He was home.

They ran up a short hill, away from the sounds of the firefight. When they got to the top, they saw a man lying down with another airman standing guard over him. The airman looked very relieved when he saw them.

"Wells," Frasier dropped to her knees next to him, digging reaching for her pack. "I'm Doctor Janet Frasier, can you hear me?" John dropped to a half crouch near the patient's head, where he could both assist Frasier and watch her back. Jackson was the only member of SG-1 that had come with them, because the rest had gone to help the other group. John was pleased to see Jackson take up a position where he could see behind John. He let Frasier take the lead, as he had no experience with these kinds of weapons.

"Yes," the injured man grunted. "It hurts so bad. I can't move, can't feel my legs. I think it went right through me."

John tried to engage him so he could focus on something other than the pain. "What's your name?"

"I'm Senior Airman Wells. Simon Wells. Am I going to die?"

"Not if I have anything to do with it," Frasier said stubbornly. "We have to flip him," she told John, who set down his rifle and got into a good position where he could grip Wells without harming him further. "Simon, you hanging in there? On three. One, two, three."

Wells grunted in pain as they rolled him. He panted and looked around wildly, subconsciously seeking something to distract him.

"My name is Doctor Watson. You're going to be fine," John assured him.

"Son of a bitch came out of nowhere," Wells said, in between gasps. "Shot me in the back."

"What's going on at home, Simon?" John asked his go-to question for distracting people from pain.

"Wife's pregnant."

"Congratulations. Will it be your first?" John asked, right before Frasier pressed on the wound. Wells grunted and gasped from the pain.

"That's good," she assured him, "At least you felt that."

Their radios crackled, and a soldier shouted over them. "Colonel O'Neill! Our positions been compromised! We're not gonna be able to hold the gate very long."

Frasier grabbed her radio as John wrapped a bandage around Well's bleeding head. "Colonel, I need more time to stabilize this patient. He can't be moved yet."

"You can't help me," Wells managed to gasp out. "Leave me!"

"Nobody is leaving you," John told him firmly.

"I'm not going to be able to see my son." Wells was preparing to give up.

John wasn't going to tolerate any of that martyr nonsense. "Hey, just focus on me! The baby will be a boy?"

Wells ignored his question. "Tell me the truth," he begged. "I'm not going to make it, right?"

"Simon, Simon! Look at me you are not going to die, okay? I did not come all the way out here for nothing. Now we've slowed the bleeding. We're gonna get you to a stretcher. We're going to get you home with your family in no time alright? Now you hang in there airman," Frasier ordered.

"Yes Ma'am," Wells said obediently.

"Good man."

John saw movement out of the corner of his eye and glanced up. He could see an alien through the trees behind Frasier. He didn't have time to grab his gun. If he let go of Wells, he could pass out from blood loss, and while it would get rid of his pain, it could lead to brain damage. "Jackson! Nine o'clock!" He prayed the archeologist was a good shot. Thankfully, Jackson didn't hesitate, just turned and shot at the enemy. His aim was good and the enemy went down.

They got the bleeding under control, and it wasn't long until two men ran up with a stretcher. The two doctors lifted Wells on it and they all hurried back to the gate. The wormhole was closed, so Jackson pushed buttons on some dial while John helped keep a look out. Over the radios he could hear an officer order a retreat to the Stargate. He heard a whooshing noise behind him, and spared a quick glance to see the gate filled with the blue goo again. Frasier and an airman carried the stretcher through the gate, while John, Jackson, and the other two airmen stayed to hold the gate. The SG teams were approaching rapidly, and John picked off the aliens coming from the sides to cut them off.

John could see Murray carrying somebody over his back. When they got closer, he was able to recognize it as O'Neill. John grimaced and hoped he wasn't dead. He was fond of the sarcastic colonel.

Murray and O'Neill were the first ones through the gate. Jackson touched John's shoulder to get his attention, and they followed them through. When they stepped into the Gateroom, John followed Murray up to the infirmary, where Frasier was giving orders left and right and airman were arriving with different injuries. He washed up and jumped right in. Here too, he was home.

* * *

"You've done us a service today, son. Doctor Jackson told me you might have saved his and Doctor Frasier's lives."

"Thank you, sir. Just doing my duty."

General Hammond pulled out a stack of papers that could make a short novel. "Of course, Doctor Watson, I'm going to need you to sign a non-disclosure agreement. Nothing related to this base, the Stargate, this program, or anything you've seen and experienced today may be discussed with anyone outside of the program, under the severest penalty."

John skimmed through the documents. Though he knew he didn't have any choice but to sign, he still wanted to know what he was getting into. Most of it was lawyer-speak, but there were a few pages that translated it all into layman's terms and outlined everything he needed to know. If only all legal documents were kind enough to do that. When he was done signing, he pushed them back towards the General.

"How much time is left in your current contract?"

John didn't need any clarification to know the General was referring to his military service. "A little under two years, sir."

"Well, son, when that's over, stop on by, and we'll sign you up here. If, of course, that's what you want. We'd be thrilled to have you. You preformed very admirably today."

"That'd be wonderful, sir," John grinned.

"I'd love to sign you up now, but I doubt your government wouldn't be very happy if we took you and didn't even tell them why. Now, if I understand correctly, you spend most of your leaves here with Doctor Frasier," Hammond waited until John nodded. "Then I suppose in the meantime, you might as well log in some off-world hours when you're on leave to get some practice in."

John didn't think it was possible to smile wider, but he was wrong. "Thank you, sir."

"You'll start out with the research groups that go to planets we've already deemed safe, but a good combat doctor like you, well, I won't be surprised if you're on one of the explorer teams within six months of joining up. I can see you going very far in this program."

"Thank you, sir, this program is just…" John searched for a suitable word but was unable to find one, "amazing."

"That it is, son. That it is."

* * *

Over the next year and a half, John spent almost all of his leave time at Cheyenne Mountain. He received training in various alien artifacts, visited a dozen or so planets, and even got in a couple of fire fights with the aliens, who he learned were called the Goa'uld. He even was able go on a few missions with SG-1. John got along famously with SG-1, and hung out with them when they were on base at the same time. It was unusual to not see them together. He also found out that Murray's real name was Teal'c, and he was actually an alien, the same type they were fighting against.

The one thing John didn't like was not being able to brag about it to his fellow soldiers when they talked about their leave. John could only shrug off their questions and claim he just spent it with family. Even his friend and nurse, Bill Murray, eventually thought he was boring. While he was still close with his squadron, all those secrets he had to keep from them, between special-ops and the Stargate, separated him from them. They slowly ceased to be family and became friends instead. He found himself feeling restless, even in the middle of a combat zone. Afghanistan wasn't enough for him once he had gotten a taste of what was really out there.

* * *

But just six months before his tour was over and he was free to join the Stargate program, John's life drastically changed in a heartbeat.

He was out on patrol in a city. Their control over it was still tenuous, and there was a possibility of insurgents that had slipped through security. It was fairly routine, and John was fully prepared for it to be boring. He wasn't even sure why he was sent with them, being one of the top surgeons at the base, though he was glad to get out.

Just a few minutes after thinking that, he was glad he was with them. They had walked into a trap.

During a brief lull in bullets, he found himself crouched over a young soldier bleeding out in the sand. The kid's leg was mangled and torn apart from a grenade, and John had no choice. He had to amputate it right there before he lost any more blood. The leg couldn't be saved. John hated amputations.

He looked at the kid, barely conscious, gasping in pain. "I'm sorry," he told him while injecting him with a medicine that would make him go numb. "I have to remove your leg."

"Doc, no please, doc, don't please, don't cut it please," the kid begged and cried in fear.

John swallowed thickly. "If I don't, you'll die. Do you want to live, soldier?"

"I want my leg," he wailed. "Please doc, save it. I thought you weren't a butcher! You're better than that, just let me keep my leg, please doc, don't chop it."

John sighed in relief when the kid finally passed out as the medicine took effect. He had only done one amputation before, and the amputee had thanked John for making that difficult choice and saving his life. Doctors performed amputations weren't well liked by the other soldiers. They were called butchers and weren't fully trusted. Unfortunately, many doctors used amputations as an easy way out of a difficult surgery, and John wasn't one of them. He steeled himself before he took the bone saw to the man's leg. He knew he was saving the kid's live, but he was a doctor and was supposed to heal people, not chop them up.

Just as he was in the middle of wrapping up the stump, he felt a sharp pain through his shoulder. John knew what it was, but he couldn't stop working on the kid to tend to himself. He tried to grit his teeth, shake it off, and keep going, but his vision quickly went fuzzy and he became light headed. He pressed one hand to the wound to stop the bleeding, and almost blacked out from the pain. He tried to finish wrapping up the kid one handed, but he had trouble focusing his vision and slumped over, passed out before he could finish.

* * *

John woke up in the hospital with a messed up shoulder and an infection in his intestines, making it hard keep food down, which caused him to lose a dangerous amount of weight. To make matters even worse, he discovered the kid didn't make it. If he could have lasted just a few minutes longer, the kid would be alive. The last few minutes of his life was spent begging John to spare his leg, and it was all for nothing. John stayed on base until the infection passed, then was shipped home to England, where he only became worse. He developed a tremor in his hands, and when he tried to walk, his leg was filled with pain and couldn't support him. John, a top surgeon in the RAMC, who was in quite a few special-ops mission, and who actually traveled throughout the galaxy to fight aliens, had shaking hands and needed a goddamned _cane_.

The only three things he truly loved were ripped from him. With his hands and leg, he was no longer able to be a surgeon and save lives, his lifelong dream. He was no longer able to function in the army, where he thrived and felt alive. He was no longer able to join the Stargate program, at least not as anything other than an advisor. John knew he couldn't stay on earth, watching teams leave through the gate without him to explore the galaxy.

He even lost Harry. While they had never been close, they were still family. But Harry and Clara were wrapped up in their divorce, and Harry spent all her free time getting drunk. John fell into a depression and pushed away all his friends. He was ashamed of himself, and ignored all attempts by people trying to get in touch, until even his Aunt Janet and Jack gave up. Hammond was the last person to stop emailing him, but eventually the General realized John would never respond. John was alone and miserable.

He lived off his army pension and savings, staying in an old bedsit, eating mainly toast, beans, and tea, and the only human contact he had was with his useless therapist. He had a place to live, but his home was gone and he would never be able to go back again. He wouldn't even be able to afford his tiny bedsit much longer, with these London rates, and he'd rather be homeless than leave his city.

Every night, he'd walk to the park and watch the stars until early morning. Afterwards, he'd go back to his flat, then stare at his empty blog and turn his gun over in his hands. He thought often about using it, but then pictured how devastated it would make Janet and Cassie, and how disappointed in him Jack and Hammond would be. He wasn't even strong enough to end the nothingness.

John lasted in this state only a few months. During a particularly eye-opening session with his stupid therapist, he realized that nothing happened. Nothing ever happened anymore, not to him. He told himself he was going to make something happen that night. He was going to find out what happened after death.

But as John walked through the park to his bedsit, he was stopped by someone he hadn't seen since university, Mike Stamford.

Mike asked him where he was living now, and John told him he couldn't afford London on his pension.

"That's not the John Watson I know."

"I'm not that John Watson," John muttered, uncomfortably aware how true that statement really was.

"Couldn't you get a flatshare or something?"

John gave a grim smile. "Come on. Who'd want me for a flatmate?"

Mike paused, clearly considering something. "You know, you're the second person to say that to me today."

John thought about his options for a second, before deciding that nothing could be worse than how he was living now. He had nothing left to lose. "Who was the first?"

* * *

And John was right. Something did happen to him that night. Sherlock Holmes happened. When John met with Sherlock and had most of his life laid bare in front of him, he felt wonder and amazement again, and a tightness in his chest he didn't realize he had loosened. When John ran with Sherlock through London, his limp disappeared and his tremor lessened. When John shot and killed a man to rescue Sherlock, he felt the hole in his heart heal a little bit. When John and Sherlock got Chinese, he realized he found a friend. Though John doubted he'd ever truly thrive again, Sherlock would keep him alive.

* * *

**What? Was that a fixit because Frasier is a freaking BAMF and should never have died? Yes. Yes it was.**

**Like I said before, I love this universe and plan on writing more. Right now, the plan is to do a series of oneshots focusing on John at Stargate Command, and then a case fic of some sort. If you have any prompts or ideas, let me know and I'll see what I can do with it  
**

**Please review, it'd mean a lot to me!**

**This series owes its title to thepinkpenguinparty. Thank you!**


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